I marvel at my fellow commuters that can apply their makeup on the bus, train or subway. The bouncing and shifting, paired with trying to hold a mirror steady would result in a mess if I tried it. I feel the same about trying to do my makeup on a plane.
That said, if my "face" lasts me all day (and it does) it should last me through an overnight flight...and it does.
I use mascara primer under my mascara and a gel eyeliner. Everything stays put. I carry cotton swabs loaded with makeup remover, just in case something smears during the flight, which I can then address on arrival at the airports. I suspect the passport control agents have seen worse that smudged eye makeup (I consider it "smokey"
)
Freecia's suggestion of blotting sheets is a great idea if you tend to get shiny.